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- Publisher Website: 10.1038/s41588-019-0537-1
- Scopus: eid_2-s2.0-85077675544
- PMID: 31911677
- WOS: WOS:000508163500002
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Article: Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes
Title | Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes |
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Authors | |
Keywords | apoptosis binding site breast cancer cancer risk chromatin |
Issue Date | 2020 |
Publisher | Nature Research (part of Springer Nature). The Journal's web site is located at http://www.nature.com/ng/ |
Citation | Nature Genetics, 2020, v. 52 n. 1, p. 56-73 How to Cite? |
Abstract | Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes. |
Persistent Identifier | http://hdl.handle.net/10722/280251 |
ISSN | 2023 Impact Factor: 31.7 2023 SCImago Journal Rankings: 17.300 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Fachal, L | - |
dc.contributor.author | Aschard, H | - |
dc.contributor.author | Beesley, J | - |
dc.contributor.author | Kwong, A | - |
dc.contributor.author | GeMO study collaborators | - |
dc.contributor.author | EMBRace collaborators | - |
dc.date.accessioned | 2020-01-21T11:50:47Z | - |
dc.date.available | 2020-01-21T11:50:47Z | - |
dc.date.issued | 2020 | - |
dc.identifier.citation | Nature Genetics, 2020, v. 52 n. 1, p. 56-73 | - |
dc.identifier.issn | 1061-4036 | - |
dc.identifier.uri | http://hdl.handle.net/10722/280251 | - |
dc.description.abstract | Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes. | - |
dc.language | eng | - |
dc.publisher | Nature Research (part of Springer Nature). The Journal's web site is located at http://www.nature.com/ng/ | - |
dc.relation.ispartof | Nature Genetics | - |
dc.rights | This is a post-peer-review, pre-copyedit version of an article published in [insert journal title]. The final authenticated version is available online at: https://doi.org/[insert DOI] | - |
dc.subject | apoptosis | - |
dc.subject | binding site | - |
dc.subject | breast cancer | - |
dc.subject | cancer risk | - |
dc.subject | chromatin | - |
dc.title | Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes | - |
dc.type | Article | - |
dc.identifier.email | Kwong, A: avakwong@hku.hk | - |
dc.identifier.authority | Kwong, A=rp01734 | - |
dc.description.nature | link_to_OA_fulltext | - |
dc.identifier.doi | 10.1038/s41588-019-0537-1 | - |
dc.identifier.pmid | 31911677 | - |
dc.identifier.pmcid | PMC6974400 | - |
dc.identifier.scopus | eid_2-s2.0-85077675544 | - |
dc.identifier.hkuros | 308965 | - |
dc.identifier.volume | 52 | - |
dc.identifier.issue | 1 | - |
dc.identifier.spage | 56 | - |
dc.identifier.epage | 73 | - |
dc.identifier.isi | WOS:000508163500002 | - |
dc.publisher.place | United States | - |
dc.identifier.issnl | 1061-4036 | - |